Variant report

Variant	rs6970399
Chromosome Location	chr7:3762229-3762230
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10230508	1.00[CEU][hapmap];0.83[LWK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10232073	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10233235	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10243789	0.90[EUR][1000 genomes]
rs10245274	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs10248557	0.85[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs10250562	0.90[EUR][1000 genomes]
rs10251183	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10253170	0.95[EUR][1000 genomes]
rs10261179	0.85[CEU][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs10263462	0.90[EUR][1000 genomes]
rs10264235	1.00[CEU][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10266883	0.85[CEU][hapmap]
rs10270665	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10271900	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs10276392	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10480094	0.85[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs11977942	1.00[JPT][hapmap]
rs17133734	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17133739	0.85[CEU][hapmap];0.87[TSI][hapmap];0.98[EUR][1000 genomes]
rs17133774	0.85[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs17133778	0.85[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs28402987	0.90[EUR][1000 genomes]
rs28503504	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28708453	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55944228	0.90[EUR][1000 genomes]
rs56111663	0.91[EUR][1000 genomes]
rs58744635	0.93[EUR][1000 genomes]
rs59839518	0.90[EUR][1000 genomes]
rs61173285	0.93[EUR][1000 genomes]
rs62437932	0.86[EUR][1000 genomes]
rs6462250	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6945690	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6946053	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6952117	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6953733	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6958764	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs6959206	0.90[EUR][1000 genomes]
rs6967060	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6972186	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6972653	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6978942	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs6979251	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6980175	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6980395	0.90[EUR][1000 genomes]
rs73304214	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73304218	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7776614	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7785239	0.93[EUR][1000 genomes]
rs7795719	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs7802557	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs7803963	0.85[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1017868	chr7:3698885-3820159	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv887335	chr7:3700352-3766819	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1021443	chr7:3705273-3889334	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv605935	chr7:3713194-3799580	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1019582	chr7:3718061-3814514	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv538682	chr7:3718061-3814514	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv605936	chr7:3722433-3766819	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1022650	chr7:3723035-3847680	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1024704	chr7:3736254-3831859	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1031610	chr7:3744536-3838844	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3736000-3764400	Weak transcription	Aorta	Aorta
2	chr7:3755200-3770200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:3760800-3762600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr7:3761200-3762800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:3761200-3762800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:3761600-3763000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:3761800-3762400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:3761800-3762600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:3761800-3762600	Enhancers	Fetal Muscle Leg	muscle
10	chr7:3761800-3762800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr7:3761800-3763000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:3762000-3762400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr7:3762000-3762400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:3762000-3762400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr7:3762000-3762400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr7:3762000-3762400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr7:3762000-3762400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr7:3762000-3762400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:3762000-3762400	Active TSS	Brain Anterior Caudate	brain
20	chr7:3762000-3762400	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr7:3762000-3762400	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr7:3762000-3762400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr7:3762000-3762400	Active TSS	Brain Substantia Nigra	brain
24	chr7:3762000-3762400	Enhancers	Fetal Brain Female	brain
25	chr7:3762000-3762400	Enhancers	HSMM	muscle
26	chr7:3762000-3762600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:3762000-3762600	Enhancers	Primary B cells from peripheral blood	blood
28	chr7:3762000-3762600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:3762000-3762600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr7:3762000-3762800	Enhancers	Brain Cingulate Gyrus	brain
31	chr7:3762200-3762400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr7:3762200-3762400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr7:3762200-3762400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr7:3762200-3762600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:3762200-3762600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:3762200-3762600	Enhancers	Lung	lung
37	chr7:3762200-3762600	Enhancers	Pancreas	Pancrea
38	chr7:3762200-3763000	Enhancers	Fetal Lung	lung
39	chr7:3762200-3764200	Weak transcription	Right Atrium	heart

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